LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  using 1 OpenMP thread(s) per MPI task
units           real
atom_style      full
boundary        p p p
dielectric      1
special_bonds   lj/coul 0.0 0.0 1.0

pair_style      hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000  11.5
bond_style      harmonic
angle_style     harmonic
dihedral_style  harmonic
improper_style  none
kspace_style    pppm 0.001

read_data       data.dreiding
Reading data file ...
  orthogonal box = (0 0 0) to (19.99689 19.12816 19.46971)
  2 by 1 by 2 MPI processor grid
  reading atoms ...
  384 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  3 = max dihedrals/atom
  orthogonal box = (0 0 0) to (19.99689 19.12816 19.46971)
  2 by 1 by 2 MPI processor grid
  reading bonds ...
  320 bonds
  reading angles ...
  448 angles
  reading dihedrals ...
  192 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        1       
  special bond factors coul:  0        0        1       
     4 = max # of 1-2 neighbors
     3 = max # of 1-3 neighbors
     5 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.007 seconds

pair_coeff      1    1    lj/cut/coul/long        0.015200000256300         2.846421344984478
pair_coeff      1    2    lj/cut/coul/long        0.001232882795416         2.846421344984478
pair_coeff      1    3    lj/cut/coul/long        0.038019995160237         3.159705878878677
pair_coeff      1    4    lj/cut/coul/long        0.038139744011598         2.939787518071103
pair_coeff      2    2    lj/cut/coul/long     9.99999974737875e-05         2.846421344984478
pair_coeff      2    3    lj/cut/coul/long        0.003083828758188         3.159705878878677
pair_coeff      2    4    lj/cut/coul/long        0.003093541672406         2.939787518071103
pair_coeff      3    3    lj/cut/coul/long        0.095100000500679         3.472990412772877
pair_coeff      3    4    lj/cut/coul/long        0.095399530150179         3.253072051965302
pair_coeff      4    4    lj/cut/coul/long        0.095700003206730         3.033153691157727
pair_coeff      4    4    hbond/dreiding/lj  2  i  4.000    2.750000000000000      4
pair_modify     mix arithmetic
neighbor        2.0 multi
neigh_modify    every 2 delay 4 check yes
variable        input index in.ch3oh.box.dreiding
variable        sname index ch3oh.box.dreiding

compute   hb all pair hbond/dreiding/lj
variable    C_hbond equal c_hb[1] #number hbonds
variable    E_hbond equal c_hb[2] #hbond energy
thermo_style    custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify   line multi format float %14.6f

fix      1      all nve

thermo 10

run 100

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2

@Article{Intveld08,
 author =  {in 't Veld, P. J. and S. J.~Plimpton and G. S. Grest},
 title =   {Accurate and Efficient Methods for Modeling Colloidal
            Mixtures in an Explicit Solvent using Molecular Dynamics},
 journal = {Comput.\ Phys.\ Commut.},
 year =    2008,
 volume =  179,
 pages =   {320--329}
}

@article{Shire2020,
 author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},
 title = {{DEM} Simulations of Polydisperse Media: Efficient Contact
          Detection Applied to Investigate the Quasi-Static Limit},
 journal = {Computational Particle Mechanics},
 year = {2020}
@article{Monti2022,
 author = {Monti, Joseph M. and Clemmer, Joel T. and Srivastava, 
           Ishan and Silbert, Leonardo E. and Grest, Gary S. 
           and Lechman, Jeremy B.},
 title = {Large-scale frictionless jamming with power-law particle 
          size distributions},
 journal = {Phys. Rev. E},
 volume = {106}
 issue = {3}
 year = {2022}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064
For more information see https://docs.lammps.org/err0029 (src/kspace.cpp:330)
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.14207291
  grid = 3 3 3
  stencil order = 5
  estimated absolute RMS force accuracy = 0.154715
  estimated relative force accuracy = 0.00046591962
  using double precision FFTW3
  3d grid and FFT values/proc = 392 12
Generated 0 of 6 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 2 steps, delay = 4 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 13.5
  ghost atom cutoff = 13.5
  binsize = 4.25, bins = 5 5 5
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair hbond/dreiding/lj, perpetual, skip from (3)
      attributes: full, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair lj/cut/coul/long, perpetual, half/full from (3)
      attributes: half, newton on, cut 13.5
      pair build: halffull/newton
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual
      attributes: full, newton on
      pair build: full/multi
      stencil: full/multi/3d
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 11.05 | 11.05 | 11.05 Mbytes
------------ Step              0 ----- CPU =            0 (sec) -------------
TotEng   =     113.723597 KinEng   =       0.000000 Temp     =       0.000000 
PotEng   =     113.723597 E_bond   =       0.535673 E_angle  =       1.281880 
E_dihed  =       1.232497 E_impro  =       0.000000 E_vdwl   =    -125.381324 
E_coul   =     597.219735 E_long   =    -361.164864 v_E_hbond =     -69.322152 
v_C_hbond =     235.000000 Press    =    -328.847363 Volume   =    7447.236335
------------ Step             10 ----- CPU =  0.003576036 (sec) -------------
TotEng   =     113.773204 KinEng   =       1.537257 Temp     =       1.346522 
PotEng   =     112.235947 E_bond   =       0.530880 E_angle  =       1.407481 
E_dihed  =       1.084172 E_impro  =       0.000000 E_vdwl   =    -126.339883 
E_coul   =     596.742308 E_long   =    -361.189011 v_E_hbond =     -69.944278 
v_C_hbond =     240.000000 Press    =    -395.900478 Volume   =    7447.236335
------------ Step             20 ----- CPU =  0.006825018 (sec) -------------
TotEng   =     113.879291 KinEng   =       2.999580 Temp     =       2.627407 
PotEng   =     110.879711 E_bond   =       0.549156 E_angle  =       1.323582 
E_dihed  =       1.357398 E_impro  =       0.000000 E_vdwl   =    -127.482103 
E_coul   =     596.318728 E_long   =    -361.187051 v_E_hbond =     -70.088343 
v_C_hbond =     237.000000 Press    =    -487.150420 Volume   =    7447.236335
------------ Step             30 ----- CPU =   0.01033254 (sec) -------------
TotEng   =     113.587471 KinEng   =       4.369566 Temp     =       3.827412 
PotEng   =     109.217905 E_bond   =       0.416485 E_angle  =       1.294630 
E_dihed  =       1.710254 E_impro  =       0.000000 E_vdwl   =    -128.565697 
E_coul   =     595.560843 E_long   =    -361.198612 v_E_hbond =     -69.848068 
v_C_hbond =     238.000000 Press    =    -423.966912 Volume   =    7447.236335
------------ Step             40 ----- CPU =   0.01411908 (sec) -------------
TotEng   =     113.915506 KinEng   =       6.466349 Temp     =       5.664037 
PotEng   =     107.449156 E_bond   =       0.514530 E_angle  =       1.342583 
E_dihed  =       1.536929 E_impro  =       0.000000 E_vdwl   =    -129.858713 
E_coul   =     595.186403 E_long   =    -361.272576 v_E_hbond =     -69.871393 
v_C_hbond =     237.000000 Press    =    -498.152655 Volume   =    7447.236335
------------ Step             50 ----- CPU =   0.01760536 (sec) -------------
TotEng   =     113.787835 KinEng   =       8.050614 Temp     =       7.051734 
PotEng   =     105.737221 E_bond   =       0.652153 E_angle  =       1.416041 
E_dihed  =       1.363560 E_impro  =       0.000000 E_vdwl   =    -130.513518 
E_coul   =     594.139764 E_long   =    -361.320780 v_E_hbond =     -69.593967 
v_C_hbond =     233.000000 Press    =    -557.299815 Volume   =    7447.236335
------------ Step             60 ----- CPU =   0.02112265 (sec) -------------
TotEng   =     114.120938 KinEng   =      10.318793 Temp     =       9.038489 
PotEng   =     103.802145 E_bond   =       0.576578 E_angle  =       1.285008 
E_dihed  =       1.123936 E_impro  =       0.000000 E_vdwl   =    -131.268312 
E_coul   =     593.450006 E_long   =    -361.365070 v_E_hbond =     -70.107165 
v_C_hbond =     238.000000 Press    =    -571.907195 Volume   =    7447.236335
------------ Step             70 ----- CPU =   0.02545985 (sec) -------------
TotEng   =     113.836168 KinEng   =      11.873184 Temp     =      10.400019 
PotEng   =     101.962984 E_bond   =       0.633521 E_angle  =       1.315999 
E_dihed  =       1.055318 E_impro  =       0.000000 E_vdwl   =    -131.673572 
E_coul   =     592.039201 E_long   =    -361.407483 v_E_hbond =     -70.518544 
v_C_hbond =     240.000000 Press    =    -576.731420 Volume   =    7447.236335
------------ Step             80 ----- CPU =   0.02924515 (sec) -------------
TotEng   =     113.589444 KinEng   =      13.546466 Temp     =      11.865689 
PotEng   =     100.042978 E_bond   =       0.637759 E_angle  =       1.439918 
E_dihed  =       1.020307 E_impro  =       0.000000 E_vdwl   =    -131.980346 
E_coul   =     590.365887 E_long   =    -361.440548 v_E_hbond =     -71.174370 
v_C_hbond =     245.000000 Press    =    -735.254245 Volume   =    7447.236335
------------ Step             90 ----- CPU =   0.03272071 (sec) -------------
TotEng   =     114.100563 KinEng   =      15.870735 Temp     =      13.901574 
PotEng   =      98.229828 E_bond   =       0.724671 E_angle  =       1.435914 
E_dihed  =       1.028167 E_impro  =       0.000000 E_vdwl   =    -132.680267 
E_coul   =     589.225622 E_long   =    -361.504279 v_E_hbond =     -72.653223 
v_C_hbond =     245.000000 Press    =    -820.598956 Volume   =    7447.236335
------------ Step            100 ----- CPU =   0.03621664 (sec) -------------
TotEng   =     113.670040 KinEng   =      17.406803 Temp     =      15.247054 
PotEng   =      96.263236 E_bond   =       0.711253 E_angle  =       1.338059 
E_dihed  =       1.474770 E_impro  =       0.000000 E_vdwl   =    -132.917719 
E_coul   =     587.219019 E_long   =    -361.562145 v_E_hbond =     -74.299795 
v_C_hbond =     246.000000 Press    =    -786.245952 Volume   =    7447.236335
Loop time of 0.036229 on 4 procs for 100 steps with 384 atoms

Performance: 238.483 ns/day, 0.101 hours/ns, 2760.223 timesteps/s, 1.060 Matom-step/s
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.020183   | 0.024045   | 0.0292     |   2.1 | 66.37
Bond    | 0.00039522 | 0.00044665 | 0.00047275 |   0.0 |  1.23
Kspace  | 0.0039474  | 0.0090708  | 0.012893   |   3.4 | 25.04
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0022867  | 0.0023574  | 0.00243    |   0.1 |  6.51
Output  | 0.00010591 | 0.00011576 | 0.00013914 |   0.0 |  0.32
Modify  | 5.0885e-05 | 5.4201e-05 | 5.8674e-05 |   0.0 |  0.15
Other   |            | 0.0001392  |            |       |  0.38

Nlocal:             96 ave         104 max          87 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost:        3063.25 ave        3108 max        3024 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs:        25463.5 ave       28799 max       22471 min
Histogram: 1 0 0 1 0 1 0 0 0 1

Total # of neighbors = 101854
Ave neighs/atom = 265.24479
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00
